I just recovered from this highly frustrating issue.
In my case, after a clog cleanup that required the cutter arm allen screw to be released and retightened, the cutter arm was hitting the side of the middle housing. The cutting process started making a loud noise, but since I had the printer for only a week, I didn’t know if this was expected or not.
So, the filament was being cut, but when the motor pushed the head to the cutter knob hard, it disturbed the X-axis positioning.
After much research and observation, I diagnosed the issue and disassembled the cutter arm several times till we found an orientation (tbh by luck) that it was able to push clear the housing.
This was a nightmare. Bambu could not help at all, but now they are providing middle housing cover and a new cutter arm.
Your my hero 
I know this is an older issue to be commenting on but I do have a piece of info that may help some people experiencing this as I just did. Running the latest firmware available for my A1 and latest Bambu Labs software I experienced this exact issue. After filament exchange the print would shift 2.5MM in the X axis. I tried moving the print to a different area of the bed. This did not help. Next I tried rotating the part on the Z axis 5 degrees. The layer shift disappeared after this with no other changes made.
I work in a precision sheet metal fabrication shop and have experienced similar issues with programming systems for million dollar lasers. Often times rotating the part 1 degree or more will make the programming issue disappear.